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Hello Barbara, I'm so sorry to hear the Blue Tit nestlings have died. The behaviour you describe by the adult sounds fairly normal when nesting; they often peck around the inside and outside of nestbox, shuffle around as they arrange the nesting materials and also as they do housekeeping to remove fecal sacs as the nestlings poop. It is often hard to say why precisely nestlings die and it could be due to a number of reasons; perhaps it was due to what the adults were feeding the nestlings, or then again it could be due to position of box, either overheating or too cold. If the adults are suffering a similar fate as you suggest then I think it could be more to do with the food they have eaten. You never know in the neighbourhoood if people have used poisons (for rodents for example) or other people feeding birds have old or moldy seeds or dirty feeders which carry harmful bacteria.
Nestlings can also suffer if one of the adult birds has died leaving only one to feed the hungry chicks. Each blue tit chick can eat up to 100 caterpillars a day so it takes both parent birds to keep up the feeding regime although if an adult is left on its own it will continue to feed the chicks - natures instinct. it would be hard if there was only one adult feeding 10 chicks for example and would expect some to die, although to lose all the birds it sounds due to more catastrophic reasons.
Regarding the cleaning of the box, it is illegal to do this at the moment whilst nesting season is still ongoing so I would leave it till end of August or September before you take the boxes to empy and clean them. Once again, I am very sorry as I know how upsetting it can be.
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Regards, Hazel